Introduction

This report takes a list of DOIs of EMBL-authored publications and extracts the countries from author affiliations on the publications in order to look at EMBL-author collaboration at the country scale.

Import the DOIs, country names and EMBL affiliations

DOIs should be provided as a single .CSV file with one column with heading ‘Doi’. DOIs that aren’t available in Europe PMC are automatically removed.

To extract the countries from the affiliations, a list of countries along with their associated continents and country codes is used. US state names are also included, as US-authors routinely do not add ‘USA’ or ‘United States’ etc. in the affiliation.

To determine which affiliations belong to EMBL authors (and therefore not a collaborating country), a list of EMBL name variations is imported. The two names used are: “EMBL” and “European Molecular Biology Laboratory”.

Retriving affiliations from Europe PMC

By querying the Europe PMC Articles API, we can retrieve all affiliations for each of the DOIs.

Then we can extract the country names from the affiliations, and check whether or not the affiliation corresponds to an EMBL affiliation.

The results are exported to a .CSV file (embl_countries.csv).

Collaborations by country and continent

From the results, we can count how many articles contain one or more affiliations from a particular country (that isn’t an EMBL affiliation). If there are multiple affiliations from a country, these are counted as a single collaboration with that country.

As plotted on an interactive world map:

And more broadly by continent: